The authors report that low percentages of dimethylsulfoxide ( DMSO ) in liquid chromatography solvents lead to a strong enhancement of electrospray ionization of peptides, improving the sensitivity of protein identification in bottom up proteomics by up to tenfold. The method can be easily implemented on any LC-MS/MS system without modification to hardware or software and at no additional cost.

An LC-MS method based on iTRAQ labeling and high resolution FT-OrbiTrap mass spectrometry was used for the proteomic analysis of 23 human ThinPrep cervical smear specimens. The analysis of three 8-plex sample sets yielded the identification of over 3200 unique proteins at FDR < 1%, of which over 2300 proteins were quantitatively profiled in at least one of the three experiments.

Weak anion exchange ( WAX ) separation of a single SCX fraction, derived from a phosphopeptide enriched sample results in more phosphopeptide Ids than SCX fractionation alone, using the same measurement time.

7.01E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

6.88E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.71E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.02E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.84E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.76E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.66E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.19E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.06E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.04E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.99E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.85E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.84E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.84E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.79E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.63E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.59E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.58E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.58E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.49E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.34E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.33E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.22E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.21E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.19E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.09E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.06E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.04E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.04E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.98E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.98E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.96E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.91E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.91E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.9E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.87E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.85E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.81E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.8E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.77E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.76E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.76E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.71E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.64E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.53E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.5E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.48E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.44E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.42E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.4E2Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.